2020-06-12 System Design update

System jacobian discussion / matrix stuff

A jacobian is a matrix where each element is a function (partial derivatives)

It just so happens that, in the FF world, most of the time these evaluate to 1 or 0

In FF-land, the jacobian matrix is “change in system parameter wrt change in FF parameter”

parameterization: R^P -> R^Q


Jacobian of parameterization: R^P -> R^PxQ


Energies: R^N->R^1


Jacobian of Energy (forces): R^N->R^N

JW – Why is jacobian of parameterization so high-dimension on the right? Shouldn’t it just be R^Q as well?

YTZ – Jacobian of parameterization has high right dimension because it prepares for worst-case situation where parameters are eg. squared or combined with each other

JW – Is a function different from a matrix?

YTZ – Yes. It can include derivatives and other non-matrixy things

Prototype update

Slots intro

(Jeff talked about how we can’t know, just from the topology, how many system parameters will be applied in some cases, eg impropers)

YTZ – We’ve run into this too. We’re handling it somewhat by separating the problem by force type. So

• R^P -> R^Q, where we call Q “system parameters"


• R^P -> R^BOND_Q,

• 
R^P -> R^ANGLE_Q

• 
R^P -> R^TORSION_Q

• 
R^P -> R^GB_Q


• R^P -> R^ES_Q

This way, we can at least isolate this uncertainty to CERTAIN parameter types, and make safe assumptions about the value of Q for others.

JW – Keep in mind that this means that analytical differentiation for SMIRKS changes in some parameter types is impossible.